A big data approach to function prediction of metabolites by clustering of structural similarity networks

2017 Fiscal Year Research-status Report

• Project/Area Number: 17K00406
• Research Institution: Nara Institute of Science and Technology
• Principal Investigator: AMIN MD.ALTAFUL 奈良先端科学技術大学院大学, 情報科学研究科, 准教授 (30379531)
• Project Period (FY): 2017-04-01 – 2020-03-31
• Keywords: Metabolomics / Metabolic Network / Metabolite Activity / Systems Biology / Network Clustering

Outline of Annual Research Achievements

Under this project, we collected metabolite activity data and structural information of metabolites from KNApSAcK database and constructed the structural similarity based network of metabolites. Also we developed a network clustering tool called DPClusOST which we will apply for function prediction of metabolites. Based on the research related to this project, we got the six publications during last one year.

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

The research is going on according to plan. We completed data collection and initial steps of the work. Also we developed a software tool called DPClusOST which will be used for function prediction of metabolites. These works resulted in the following publications

I. Nobutaka Wakamatsu, Tsuyoshi Shirai, Ryohei Eguchi, Mohammad Bozlul Karim, Naoaki Ono, Shigehiko Kanaya and Md. Altaf-Ul-Amin, “A Network based Approach to Predict Functions of Metabolites”, International Conference on Metabolomics, 2018, Bangkok (Poster).

II. Mohammad Bozlul Karim, Nobutaka Wakamatsu and Md. Altaf-Ul-Amin, "DPClusOST: A Software Tool for General Purpose Graph Clustering", Journal of Computer Aided Chemistry, Vol. 18, 76-93,(2017).

Strategy for Future Research Activity

This year we are conducting experiments and preparing the manuscript of a journal paper titled as follows: “An approach to function prediction of metabolites by clustering the 3D-chemical structural similarity based network”. We hope to submit it within next 6 months. After that we will proceed to development of iterative function prediction step and validation of our predictions and eventually will write another journal paper.

Research Products

• [Journal Article] Metabolite-Content-Guided Prediction of Medicinal/Edible Prop-erties in Plants for Bioprospecting (2018)
  • Author(s): Liu, K., Morita, A. H., Kanaya, S., & Atlaf-Ul-Amin, M.
  • Journal Title: Curr Res Complement Altern Med Volume: 130 Pages: 1-15
  • DOI: 10.29011. CRCAM-130/100030
• [Journal Article] Metabolomic Studies of Indonesian Jamu Medicines: Prediction of Jamu Efficacy and Identification of Important Metabolites (2017)
  • Author(s): Sony Hartono Wijaya, Irmanida Batubara, Takaaki Nishioka, Md. Altaf-Ul-Amin, and Shigehiko Kanaya
  • Journal Title: Molecular Informatics Volume: 36 Pages: 1-16
  • DOI: 10.1002/minf.201700050
• [Journal Article] Classification of Alkaloid Compounds Based on Subring Skeleton (SRS) Profiling: On Finding Relationship of Compounds with Metabolic Pathways (2017)
  • Author(s): Eguchi, R., Ono, N., Horai, H., Amin, M. A. U., Hirai, A. M., Kawahara, J., ... & Kanaya, S.
  • Journal Title: Journal of Computer Aided Chemistry Volume: 18 Pages: 58-75
  • DOI: https://doi.org/10.2751/jcac.18.58
• [Journal Article] DPClusOST: A Software Tool for General Purpose Graph Clustering (2017)
  • Author(s): Mohammad Bozlul Karim, Nobutaka Wakamatsu and Md. Altaf-Ul-Amin
  • Journal Title: Journal of Computer Aided Chemistry Volume: 18 Pages: 76-93
  • DOI: 10.2751/jcac.18.76
• [Presentation] A Network based Approach to Predict Functions of Metabolites (2018)
  • Author(s): Md. Altaf-Ul-Amin
  • Organizer: International Conference on Metabolomics,
  • Int'l Joint Research
• [Presentation] Multifaceted analysis of sequence similarity based network of allergens (2018)
  • Author(s): Yasue Aoyama
  • Organizer: International Conference on Computational Mathematics , Physics and It's Applications
  • Int'l Joint Research